Single-cell RNA-seq-based proteogenomics identifies glioblastoma-specific transposable elements encoding HLA-I-presented peptides

Transposable Element Regulation and Expression in Cancer

(2021) Erin E. Grundy et al.   FEBS Journal

Very low mutation burden is a feature of inflamed recurrent glioblastomas responsive to cancer immunotherapy

(2021) Matthias Gromeier et al.   Nature Communications

Identifying transposable element expression dynamics and heterogeneity during development at the single-cell level with a processing pipeline scTE

(2021) Jiangping He et al.   Nature Communications

High tumor mutation burden fails to predict immune checkpoint blockade response across all cancer types

(2021) D.J. McGrail et al.   ANNALS OF ONCOLOGY

Promises and challenges of adoptive T-cell therapies for solid tumours

(2021) Matteo Morotti et al.   BRITISH JOURNAL OF CANCER

Atypical acute myeloid leukemia-specific transcripts generate shared and immunogenic MHC class-I-associated epitopes

(2021) Grégory Ehx et al.   IMMUNITY

ORFik: a comprehensive R toolkit for the analysis of translation

(2021) Håkon Tjeldnes et al.   BMC BIOINFORMATICS

Proteogenomics Uncovers a Vast Repertoire of Shared Tumor-Specific Antigens in Ovarian Cancer

(2020) Qingchuan Zhao et al.   Cancer Immunology Research

Activation of a Subset of Evolutionarily Young Transposable Elements and Innate Immunity are Linked to Clinical Responses to 5-Azacytidine

(2020) Hitoshi Ohtani et al.   CANCER RESEARCH

Integrated proteogenomic deep sequencing and analytics accurately identify non-canonical peptides in tumor immunopeptidomes

(2020) Chloe Chong et al.   Nature Communications

Reawakening the Developmental Origins of Cancer Through Transposable Elements

(2020) Chiemi F. Lynch-Sutherland et al.   Frontiers in Oncology

Measuring and interpreting transposable element expression

(2020) Sophie Lanciano et al.   NATURE REVIEWS GENETICS

CIITA-transduced glioblastoma cells uncover a rich repertoire of clinically relevant tumor-associated HLA-II antigens

(2020) Greta Forlani et al.   MOLECULAR & CELLULAR PROTEOMICS

Vestigial-like 1 is a shared targetable cancer-placenta antigen expressed by pancreatic and basal-like breast cancers

(2020) Sherille D. Bradley et al.   Nature Communications

Transcript assembly improves expression quantification of transposable elements in single-cell RNA-seq data

(2020) Wanqing Shao et al.   GENOME RESEARCH

Adenovirus based virus-like-vaccines targeting endogenous retroviruses can eliminate growing colorectal cancers in mice

(2019) Lasse Neukirch et al.   Oncotarget

Transposable element expression in tumors is associated with immune infiltration and increased antigenicity

(2019) Yu Kong et al.   Nature Communications

A large peptidome dataset improves HLA class I epitope prediction across most of the human population

(2019) Siranush Sarkizova et al.   NATURE BIOTECHNOLOGY

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Identification of tumor antigens among the HLA peptidomes of Glioblastoma tumors and plasma

(2018) Bracha Shraibman et al.   MOLECULAR & CELLULAR PROTEOMICS

Endogenous retroviral signatures predict immunotherapy response in clear cell renal cell carcinoma

(2018) Christof C. Smith et al.   JOURNAL OF CLINICAL INVESTIGATION

The Immune Epitope Database (IEDB): 2018 update

(2018) Randi Vita et al.   NUCLEIC ACIDS RESEARCH

Noncoding regions are the main source of targetable tumor-specific antigens

(2018) Céline M. Laumont et al.   Science Translational Medicine

Transposable Elements in Human Cancer: Causes and Consequences of Deregulation

(2017) Sumadi Anwar et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

DNMT and HDAC inhibitors induce cryptic transcription start sites encoded in long terminal repeats

(2017) David Brocks et al.   NATURE GENETICS

Tumor Mutational Burden and Response Rate to PD-1 Inhibition

(2017) Mark Yarchoan et al.   NEW ENGLAND JOURNAL OF MEDICINE

Single-Cell RNA-Seq Analysis of Infiltrating Neoplastic Cells at the Migrating Front of Human Glioblastoma

(2017) Spyros Darmanis et al.   Cell Reports

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

The impact of transposable elements on mammalian development

(2016) Jose L. Garcia-Perez et al.   DEVELOPMENT

A hot L1 retrotransposon evades somatic repression and initiates human colorectal cancer

(2016) Emma C. Scott et al.   GENOME RESEARCH

Human Leukocyte Antigen (HLA) Peptides Derived from Tumor Antigens Induced by Inhibition of DNA Methylation for Development of Drug-facilitated Immunotherapy

(2016) Bracha Shraibman et al.   MOLECULAR & CELLULAR PROTEOMICS

Global proteogenomic analysis of human MHC class I-associated peptides derived from non-canonical reading frames

(2016) Céline M. Laumont et al.   Nature Communications

gEVE: a genome-based endogenous viral element database provides comprehensive viral protein-coding sequences in mammalian genomes

(2016) So Nakagawa et al.   Database-The Journal of Biological Databases and Curation

TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets

(2015) Ying Jin et al.   BIOINFORMATICS

Molecular and Genetic Properties of Tumors Associated with Local Immune Cytolytic Activity

(2015) Michael S. Rooney et al.   CELL

DNA-Demethylating Agents Target Colorectal Cancer Cells by Inducing Viral Mimicry by Endogenous Transcripts

(2015) David Roulois et al.   CELL

TIGIT and PD-1 impair tumor antigen–specific CD8+ T cells in melanoma patients

(2015) Joe-Marc Chauvin et al.   JOURNAL OF CLINICAL INVESTIGATION

Pooled Analysis of Long-Term Survival Data From Phase II and Phase III Trials of Ipilimumab in Unresectable or Metastatic Melanoma

(2015) Dirk Schadendorf et al.   JOURNAL OF CLINICAL ONCOLOGY

Retrotransposon insertions in the clonal evolution of pancreatic ductal adenocarcinoma

(2015) Nemanja Rodić et al.   NATURE MEDICINE

NY-ESO-1–specific TCR–engineered T cells mediate sustained antigen-specific antitumor effects in myeloma

(2015) Aaron P Rapoport et al.   NATURE MEDICINE

PD-1 Blockade in Tumors with Mismatch-Repair Deficiency

(2015) Dung T. Le et al.   NEW ENGLAND JOURNAL OF MEDICINE

Immunogenicity of somatic mutations in human gastrointestinal cancers

(2015) E. Tran et al.   SCIENCE

A dendritic cell vaccine increases the breadth and diversity of melanoma neoantigen-specific T cells

(2015) B. M. Carreno et al.   SCIENCE

Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer

(2015) N. A. Rizvi et al.   SCIENCE

Chromosome 7 gain and DNA hypermethylation at the HOXA10 locus are associated with expression of a stem cell related HOX-signature in glioblastoma

(2015) Sebastian Kurscheid et al.   GENOME BIOLOGY

Cytotoxicity of Human Endogenous Retrovirus K-Specific T Cells toward Autologous Ovarian Cancer Cells

(2014) K. Rycaj et al.   CLINICAL CANCER RESEARCH

Checkpoint blockade cancer immunotherapy targets tumour-specific mutant antigens

(2014) Matthew M. Gubin et al.   NATURE

Genetic Basis for Clinical Response to CTLA-4 Blockade in Melanoma

(2014) Alexandra Snyder et al.   NEW ENGLAND JOURNAL OF MEDICINE

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

The Somatic Genomic Landscape of Glioblastoma

(2013) Cameron W. Brennan et al.   CELL

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

Mining exomic sequencing data to identify mutated antigens recognized by adoptively transferred tumor-reactive T cells

(2013) Paul F Robbins et al.   NATURE MEDICINE

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Exploiting the Mutanome for Tumor Vaccination

(2012) J. C. Castle et al.   CANCER RESEARCH

Vaccination with Cancer- and HIV Infection-Associated Endogenous Retrotransposable Elements Is Safe and Immunogenic

(2012) J. B. Sacha et al.   JOURNAL OF IMMUNOLOGY

Parallel detection of antigen-specific T cell responses by combinatorial encoding of MHC multimers

(2012) Rikke Sick Andersen et al.   Nature Protocols

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Human Endogenous Retrovirus K Triggers an Antigen-Specific Immune Response in Breast Cancer Patients

(2008) F. Wang-Johanning et al.   CANCER RESEARCH

CTdatabase: a knowledge-base of high-throughput and curated data on cancer-testis antigens

(2008) L. G. Almeida et al.   NUCLEIC ACIDS RESEARCH